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Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). Wtdbg2 has two key components: an assembler wtdbg2 and a consenser wtpoa-cns. Executable wtdbg2 assembles raw reads and generates the contig layout and edge sequences in a file "prefix.ctg.lay.gz". Executable wtpoa-cns takes this file as input and produces the final consensus in FASTA.
Quick Start
- To use wtpoa-cns, input must be the <prefix>.ctg.lay.gz file(s) output from wtdbg2
- Resources: https://github.com/ruanjue/wtdbg2
Test Data
Input File(s)
Use wtdbg2wtdbg_SRR8506728_L5000_output.ctg.lay.gz as the input file.
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
- Set output file name to wtpoa-cnsto wtpoa_SRR8506728_L5000_output.fa
- All other parameters should be left as default
Output File(s)
This analysis will generate a single FASTA formatted output file of consensus contigs (named as indicated above):
wtpoa-cns_SRR8506728_L5000_output.fa